Another thing I have implemented is a custom setting referenced in workflows & triggers to determine whether to perform various actions (specifically sending emails)
something similar to this:
It was a bugger to get implemented since there were tons of workflows, triggers, and controllers to update. Now I'm very glad I took the time to do it.
You have to remember to set default org values though since custom settings don't get populated in a sandbox refresh. As of Summer 13 custom settings get copied to sandboxes.